Contacts of the strand formed by residues 338 - 341 (chain D) in PDB entry 4RYD
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 338 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316D SER 3.6 2.8 + - - -
317D ILE* 3.4 14.6 - - + +
318D SER 2.9 22.0 + - - -
336D THR* 3.6 4.4 - - - +
337D LEU* 1.3 80.2 - - - +
339D THR* 1.3 66.9 + - - +
397D VAL* 3.5 25.8 - - + -
401D SER* 3.7 4.5 - - - +
424D TYR 3.4 8.7 - - - -
426D TYR 4.3 0.4 - - - +
427D GLY 3.5 7.6 - - - +
429D LEU* 3.5 17.7 - - + -
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Residues in contact with THR 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317D ILE* 4.2 0.2 - - - -
318D SER* 3.4 16.4 - - - +
319D SER 3.5 19.7 - - - +
320D ALA* 3.7 13.2 - - + +
338D ALA* 1.3 75.7 + - - +
340D THR* 1.3 79.8 + - - +
406D LEU* 4.7 0.7 - - + -
424D TYR* 2.8 42.3 + - + -
427D GLY 2.7 20.0 + - - -
428D LEU* 3.4 8.6 - - + -
429D LEU* 2.9 26.7 + - - +
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Residues in contact with THR 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D LEU* 4.0 13.7 - - + -
317D ILE* 3.8 7.6 - - + -
318D SER 3.1 3.6 + - - -
319D SER* 3.3 1.4 - - - -
320D ALA 3.3 14.4 + - - -
339D THR* 1.3 83.9 - - - +
341D TYR* 1.3 63.1 + - - +
370D SER* 2.9 54.7 + - - +
373D LEU* 4.2 11.8 - - + +
374D ALA* 3.9 8.5 - - + +
428D LEU* 4.1 2.0 - - - -
429D LEU* 3.6 26.7 - - + -
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Residues in contact with TYR 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D TRP* 3.5 31.0 - + + -
123D TYR* 3.9 21.1 - - + -
130D ARG* 3.4 30.8 + - + +
131D ASP* 3.5 22.7 - - - -
132D LEU* 4.1 14.0 - - + +
320D ALA* 3.4 16.6 - - + -
321D THR 3.5 26.5 - - - -
322D GLN 4.2 5.2 + - - -
324D GLY* 4.9 2.2 - - - -
340D THR* 1.3 77.2 - - - +
342D SER* 1.3 61.9 + - - +
351D ILE* 4.0 2.4 - - - +
369D ALA 4.5 0.2 - - - +
370D SER* 3.6 4.0 + - - -
373D LEU* 3.4 21.2 - - + +
405D HIS* 5.1 3.8 - - - +
406D LEU* 4.7 6.1 - - + +
428D LEU* 3.2 33.4 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il